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Previously, Deuterostomia also included the phyla Brachiopoda, Bryozoa, Chaetognatha, and Phoronida based on embryological characteristics. However, Superphylum Deuterostomia was redefined in 1995 based on DNA molecular sequence analyses when the lophophorates were removed from it and combined with other protostome animals to form superphylum Lophotrochozoa.[4] The phylum Chaetognatha (arrow worms) may belong here, but molecular studies have placed them in the protostomes more often.

In both deuterostomes and protostomes, a zygote first develops into a hollow ball of cells, called a blastula. In deuterostomes, the early divisions occur parallel or perpendicular to the polar axis. This is called radial cleavage, and also occurs in certain protostomes, such as the lophophorates.

Most deuterostomes display indeterminate cleavage, in which the developmental fate of the cells in the developing embryo are not determined by the identity of the parent cell. Thus, if the first four cells are separated, each cell is capable of forming a complete small larva; and if a cell is removed from the blastula, the other cells will compensate.

Another feature present in both the Hemichordata and Chordata is pharyngotremy; the presence of spiracles or gill slits into the pharynx, which is also found in some primitive fossil echinoderms (mitrates).[5][6] A hollow nerve cord is found in all chordates, including tunicates (in the larval stage). Some hemichordates also have a tubular nerve cord. In the early embryonic stage, it looks like the hollow nerve cord of chordates.

Because of the highly modified nervous system of echinoderms, it is not possible to discern much about their ancestors in this matter, but based on different facts it is quite possible that all the present deuterostomes evolved from a common ancestor that had pharyngeal gill slits, a hollow nerve cord, circular and longitudinal muscles and a segmented body.[7] It could have resembled the small group of Cambrian urochordate deuterostomes named Vetulicolia.

The defining characteristic of the deuterostome is the fact that the blastopore (the opening at the bottom of the forming gastrula) becomes the anus, whereas in protostomes the blastopore becomes the mouth. The deuterostome mouth develops at the opposite end of the embryo from the blastopore and a digestive tract develops in the middle, connecting the two.

In many animals these early development stages later evolved in ways that no longer reflect these original patterns. For instance, humans have already formed a gut tube at the time of formation of the mouth and anus. Then the mouth is formed first, during the fourth week of development, and the anus is created four weeks later, temporarily forming a cloaca.

The majority of animals more complex than jellyfish and other Cnidarians are split into two groups, the protostomes and deuterostomes. Chordates (which include all the vertebrates) are deuterostomes.[8] It seems likely that the 555 million year oldKimberella was a member of the protostomes.[9][10] That implies that the protostome and deuterostome lineages split some time before Kimberella appeared — at least 558 million years ago, and hence well before the start of the Cambrian 541 million years ago,[8]i.e. during the later part of the Ediacaran Era (circa 635-542 Mya, around the end of global Marinoan glaciation in the late Neoproterozoic). The oldest discovered proposed deuterostome is Saccorhytus coronarius, which lived approximately 540 million years ago.[2][11] The researchers that made the discovery believe that the Saccorhytus is a common ancestor to all previously-known deuterostomes.[11]

On the other hand, fossils of early chordates are very rare, as non-vertebrate chordates have no bone tissue or teeth, and fossils of no Post-Cambrian non-vertebrate chordates are known aside from the Permian-aged Paleobranchiostoma, trace fossils of the Ordovician colonial tunicate Catellocaula, and various Jurassic-aged and Tertiary-aged spicules tentatively attributed to ascidians.

Below is a phylogenetic tree showing consensus relationships among deuterostome taxa. Phylogenomic evidence suggests the enteropneust family, Torquaratoridae, fall within the Ptychoderidae. The tree is based on 16S +18S rRNA sequence data and phylogenomic studies from multiple sources.[19] The approximate dates for each radiation into a new clade are given in millions of years ago (Mya).[20]